rs169173

Variant names:

• chr21-30632027-T-C
• rs169173

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.209 in 152,172 control chromosomes in the GnomAD database, including 4,071 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (4071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31761 AN: 152054 Hom.: 4075 Cov.: 32

Gnomad AFR AF: 0.0579

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.226

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.209 AC: 31752 AN: 152172 Hom.: 4071 Cov.: 32 AF XY: 0.208 AC XY: 15487 AN XY: 74378

African (AFR) AF: 0.0579 AC: 2406 AN: 41546

American (AMR) AF: 0.198 AC: 3028 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3468

East Asian (EAS) AF: 0.148 AC: 765 AN: 5178

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4818

European-Finnish (FIN) AF: 0.287 AC: 3035 AN: 10576

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19899 AN: 67992

Other (OTH) AF: 0.224 AC: 473 AN: 2114

Alfa AF: 0.261 Hom.: 7357

Bravo AF: 0.195

Asia WGS AF: 0.172 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.83
PhyloP100		0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs169173; hg19: chr21-32004346;